If you use the default framebuffer for layered rendering, then everything you draw will go straight to the default framebuffer. They will behave as if everything were in the same layer.
OpenGL 4.4 Core Specification - 9.8 Layered Framebuffers - pp. 296
A framebuffer is considered to be layered if it is complete and all of its populated attachments are layered. When rendering to a layered framebuffer, each fragment generated by the GL is assigned a layer number.
[...]
A layer number written by a geometry shader has no effect if the framebuffer is not layered.